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Missed chances proved costly for Gills, according to their manager Martin Allen.
A number of good opportunities went begging, particularly in the first half, and a failure to convert signalled Gills’ exit from the cup competition.
“I thought the lads did quite well to be honest,” said Allen.
“We had some good chances in the first half, four good ones, none of them which managed to go into the goal and they scored from their first and only chance.
“Fresh legs came on in the second half and I thought we played very well. There were some good passing movements, good crosses but once again we never managed to get the breaks.
“That’s both games we’ve played now where we’ve had chances and they will go in.
“The level of commitment and energy was second to none and we were up against a decent side who were in the Championship last year.
“They have some good players, there is no doubt about that. We play them in a few weeks in the league and so that one is a game I look forward to.”
Allen made five changes to his starting eleven. Some were enforced and others were with an eye on Saturday’s League 1 trip to Wolves.
“There was only 14 players (training) on Monday so it is a little bit tight,” he said.
“The players do need to play, they have to play and these opportunities come along and you have to have faith in all of your players and I have.
“I rested a few players, which is obvious.”
Among those rested was Amine Linganzi. Charlie Lee was on the bench despite sitting out training the previous day with a bruised foot. Charlie Allen remains sidelined with a foot injury.
The Gills had to sit back at times as City passed the ball around but Allen accepts that is what will happen at the higher level.
He said: “There are times when clubs, with the resources and the players that these teams have, are at times going to be able to keep the ball and move it around the pitch. You have to be patient and wait.
“They pay a lot of money for their players and sometimes you have to accept that that’s going to happen if you go up a division.
“Overall we stuck to our jobs well, we restricted them to very few chances and we had some very good opportunities in the first half and some good play, good interchanges of positions and good crossing but we just couldn’t finish them off.”